Release of Bio-Formats 7.1.0

Today we are releasing Bio-Formats 7.1.0 which includes several API additions and a number of format improvements for SVS, DICOM WSI, CV7000 and cellSens VSI.

The full list of changes included in this release are as follows:

API Additions

• ICompressedTileReader
  • a new interface allowing for the reading of compressed bytes without decompression. Currently only implemented by the SVSReader
• ICompressedTileWriter
  • a new interface allowing for the writing of precompressed bytes. Currently only implemented by the DICOM Writer
• IExtraMetadataWriter
  • a new interface enabling extra supplemental metadata to be set for inclusion in a writer. Currently only implemented by the DICOM Writer

File format fixes and improvements:

• Aperio SVS
  • added implementation for the reading of compressed data without decompression using the new ICompressedTileReader interface
• cellSens VSI
  • fixed handling of uncompressed BGR data
• CV7000
  • action index is now included in the channel name
  • Fluor will now be set on Channel when possible
  • for missing planes the default behavior has switched from returning a blank plane to returning the first plane in the channel
  • added a new reader option cv7000.duplicate_missing_planes to control the behavior for missing planes
• DICOM
  • added implementation for the writing of precompressed data using the new ICompressedTileWriter interface
  • added implementation for the writing of extra supplemental metadata data using the new IExtraMetadataWriter interface. Extra metadata can be provided in the form of a .json file
  • This functionality was implemented through collaboration between Glencoe Software and NCI Imaging Data Commons, and has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Task Order No. HHSN26110071 under Contract No. HHSN2612015000031.
• Photoshop TIFF
  • fixed plane reading with memoization

Bio-Formats improvements:

• fixed handling of JPEG Turbo service when the native library cannot be loaded, most notably for Apple Silicon instances. An IOException will now be thrown by readers that require the library but the RunTimeException introduced in 7.0.1 will no longer be thrown when the library is not required
• prevented unnecessary Lurawave debug error being printed (thanks to Can Gokhan Dogan)
• updated license headers for all Java sources of the OME-XML library
• added a new codec option disableChromaSubsampling along with implementation for the JPEG Codec (thanks to Peter Haub)
• updated github actions checkout version to v4 and build release on ubuntu 22.04
• json dependency moved from formats-gpl to formats-bsd
• TiffSaver now generates valid 4-channel RGBA images (thanks to Can Gokhan Dogan)
• added a new ` precompressed` option to the bfconvert tool, enabling the conversion of precompressed tiles. Currently only supported for converting from SVS to DICOM.
• added a new ` extra-metadata` option to the bfconvert tool for providing supplemental metadata during conversion. Currently only supported for writing to DICOM

Component updates:

• slf4j-api was upgraded to 2.0.9
• logback-classic was upgraded to 1.3.14
• logback-core was upgraded to 1.3.14
• xalan was upgraded to 2.7.3
• com.google.guava was upgraded to 32.0.0-jre
• json was upgraded to 20230227
• ome-common was upgraded to 6.0.21
• ome-model was upgraded to 6.3.4
• ome-codecs was upgraded to 1.0.1
• ome-poi was upgraded to 5.3.8
• ome-metakit was upgraded to 5.3.6

Documentation improvements:

• fixed a number of broken external links
• updated the bfconvert instructions to document new options
• added a new link for the external Bioformats.NET project